error in Viral_Track_scanning - after the step of "Export of the viral SAM file done for hgmm_100_R2_extracted "

[GhobrialMoheb]

I am getting this error (highlighted in bold:

Loading of the libraries.... Warning message:
multiple methods tables found for ‘rowRanges’
... done ! [[1]]

Warning message:
In read.table(Parameter_target_files, header = F, sep = "\t") :
incomplete final line found by readTableHeader on '/mnt/c/Users/mohebg/Desktop/Viral_Track/Target_file.txt'
1 Fastq files are going to be processed !
Mapping hgmm_100_R2_extracted.fastq file
STAR --runThreadN 20 --genomeDir /mnt/c/Users/mohebg/Desktop/newscanpyinR/index/ --readFilesIn /mnt/c/Users/mohebg/Desktop/newscanpyinR/hgmm_100_R2_extracted.fastq --outSAMattributes NH HI AS nM NM XS --outFileNamePrefix /mnt/c/Users/mohebg/Desktop//Viral_Track/Test_COVID//hgmm_100_R2_extracted/hgmm_100_R2_extracted_ --outSAMtype BAM SortedByCoordinate --twopassMode Basic --outFilterMatchNmin 35 --outFilterScoreMinOverLread 0.6 --outFilterMatchNminOverLread 0.6
STAR version: 2.7.10a compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source
Aug 03 18:28:11 ..... started STAR run
Aug 03 18:28:11 ..... loading genome
Aug 03 18:29:40 ..... started 1st pass mapping
Aug 03 18:30:06 ..... finished 1st pass mapping
Aug 03 18:30:06 ..... inserting junctions into the genome indices
Aug 03 18:31:58 ..... started mapping
Aug 03 18:32:26 ..... finished mapping
Aug 03 18:32:31 ..... started sorting BAM
Aug 03 18:32:40 ..... finished successfully
Mapping ofhgmm_100_R2_extracted.fastq done !
Warning message:
In dir.create(temp_output_dir) :
'/mnt/c/Users/mohebg/Desktop//Viral_Track/Test_COVID//hgmm_100_R2_extracted' already exists
All fastq files have been mapped successfully
Starting the BAM file analysis
Indexing of the bam file for hgmm_100_R2_extracted is done
Computing stat file for the bam file for hgmm_100_R2_extracted is done
Checking the mapping quality of each virus...
Export of the viral SAM file done for hgmm_100_R2_extracted
Error in { : task 1 failed - "different row counts implied by arguments"
Calls: %dopar% ->
In addition: Warning message:
In dir.create(paste(k, "Viral_BAM_files", sep = "")) :
'/mnt/c/Users/mohebg/Desktop//Viral_Track/Test_COVID//hgmm_100_R2_extracted/Viral_BAM_files' already exists
Execution halted

[GhobrialMoheb]

@PierreBSC , I have got a new error message:

Aug 04 15:44:28 ..... started STAR run
Aug 04 15:44:28 ..... loading genome
Aug 04 15:45:37 ..... started 1st pass mapping
Aug 04 15:46:02 ..... finished 1st pass mapping
Aug 04 15:46:02 ..... inserting junctions into the genome indices
Aug 04 15:47:38 ..... started mapping
Aug 04 15:48:05 ..... finished mapping
Aug 04 15:48:09 ..... started sorting BAM
Aug 04 15:48:17 ..... finished successfully
Mapping ofhgmm_100_R2_extracted.fastq done !
All fastq files have been mapped successfully
Starting the BAM file analysis
Indexing of the bam file for hgmm_100_R2_extracted is done
Computing stat file for the bam file for hgmm_100_R2_extracted is done
Checking the mapping quality of each virus...
Export of the viral SAM file done for hgmm_100_R2_extracted
Error in colnames<-(*tmp*, value = c("N_reads", "N_unique_reads", :
attempt to set 'colnames' on an object with less than two dimensions
Calls: colnames<- -> colnames<-
Execution halted